Tuesday, July 27, 2010

I was told by Sarah that if I did not write on the blog of the esteemed MacQueen lab, we could not be best friends. Therefore, I must post!

A few members of the MacQueen lab tentatively came into the Hingorani lab the other day to look at my microplates. In the microplates were fabulous colors (whose beauty was magnified by the photography skills of the MacQueen gang--see 'Sourjourn into Manjuland").

I am working on characterizing the kinetics of three MutS (Msh2-Msh6 in humans) mutants. MutS is a protein that recognizes mismatched DNA and recruits other proteins to initiate the DNA mismatch repair process. I am studying three cancer-associated mutants in Thermus aquaticus ("Taq"), as it is an easy organism to work with and there is high sequence homology between Taq and human MutS. In addition to binding mismatched DNA, MutS it is also an ATPase, and we're interested in the mechanism of ATP hydrolysis (ATP--> ADP + Pi) in the MutS mutants, and it is thought that MutS may communicate that it has bound a mismatch through coordination of its DNA binding site and ATPase domain.

One way to measure ATP hydrolysis is through phosphate production. The microplates that the MacQueeners photographed were part of the "Malachite Green Assay." Malachite green turns from yellow to green when it binds phosphate and this color change can be quantified. We create a standard curve with our stock of phosphate and then use this standard to calculate the concentration of phosphate at different time points in the reaction mixture that includes MutS and ATP. Using the concentration of phosphate at different time points in the reaction, we are able to determine kcat, which informs us about how fast the protein hydrolyzes ATP (more formally, kcat represents how many molecules of ATP are hydrolyzed per MutS active site per minute).

Saturday, July 24, 2010

So I would like to edit my previous post. I neglected to mention some important information; the other labs that present at the WEAST meeting are the wonderful Holmes lab, with whom we went on a hike and you will hopefully see pictures soon, and the fabulous McAlear lab. The other person presentin today (bc more than one person usually presents at WEAST) was Sarah Kass-Gergi, a brilliant undergrad from the McAlear lab. Hopefully we can convince her to write a post sometime in the future.

y THIS IS A HUGE DEAL. Dr. Manju Hingorani runs the lab next door, and I think she is kind of enigmatic, and very awesome. She keeps a little tiny tote bag stocked with chocolate hanging on the doorknob of her office, and she's always pacing around with a canteen of loose tea leaves and whispering about DNA. I'm not so sure the admiration is mu

tual, though, because in the past, Manju (who, by the way, INSISTS that everybody, students included, refer to her as Manju and gave me a death look the first [and last] time I referred to her as Dr. Hingorani) has expressed her, um, dissatisfaction with some of the more robustly-vocal-chorded undergrads of the MacQueen Lab

(one is the author of this post and the other has a nickname that rhymes with "gators")

and their propensity for emitting cackles that reverberate into her office. Given this stormy torrid drama of our past, I always thought setting foot into DNALab would be a mere dream, never to be fulfilled...

BUT NAY!!!!!!!!!!!!!!!!!!

Today after WEAST (which will be blogged about in the near future for those of you not in the know), Tatiana came galloping into our lab proclaiming "ARIEL IS DOING THINGS WITH PRETTY 96-WELL PLATES!!!!!!!!!!!!" Ariel is the awesome undergrad in Manju's lab who, as Esther informed us, placed first in her group in the Middletown 5k!! Anyway, I grabbed my camera and scurried to investigate.

HOW COOL IS THAT?!?!??!?!?!?!?!

More science eye candy:

I know at this point you're probably thinking "Wow, that IS pretty, but what IS it?" (either that or "This girl needs to get out more"), and I am embarrassed to say that in my haste to get back to work (okay, it was actually because Ariel made us leave), I didn't ask her what exactly these were for. But I PROMISE I will find out and update next week because I know you're all as curious as I am!!!!!!!

P.S.: Get excited for a SUPER-SCIENTIFIC (seriously!) post tomorrow about the biochemistry behind SPORULATION! It's one of the most useful and important techniques that we use in our lab, but admit it, do you really know why putting yeast into media containing potassium acetate makes them enter meiosis (beyond "it starves them")? FIND OUT HERE TOMORROW!! (I was actually going to write this post tonight, but then I ended up spending more than an hour JUST ON THE RESEARCH. This is legit, folks!)

Hey y'all! I'm writing a breif entry about our WEAST meeting. Since everyone has been scolding me for not having blogged yet, I figured better a short entry than no entry at all.

Today we had our last WEAST meeting of the summer :(. As sarah would say, sad day. WEAST meetings are these wonderful meetings that we've organized with some of the other labs that use yeast ( hence weast, wes yeast). They are super helpful for learning how to present your material to others, dealing with questions and troubleshooting. I think it is very nice to have meetings with people who know the organism and can bring different perspectives and advice to the table on a particular project.

Since today was our last day of the summer we had tons of food (nom nom). Rozina and I presented the work that we have been doing, which is basically to create a tool, in our case a temperature sensative allele, that will allow us to investigate the role of Zip2, Zip3 and Zip4 in synaptonemal complex, the protein that holds homologs together during Meiosis I. In case you were wondering what the above picture is, it was a drawing I did for our presentation of abnormal and normal synaptonemal complex.

I think the presentation went more or less smoothly, there were a couple of questions that I had some difficulty with but overall it was a great learning experience. We have presented our work a few times now and each time we learn something new about how to present, or the content itself. I hope that WEAST will be able to continue into the year and I think that it's the kind of meeting that all labs should be doing in their field on a regular basis because it promotes sharing of information, ideas and thereby progress and forward momentum

Thursday, July 22, 2010

Yesterday Amy and I ran a 5k race in middletown with some other MB&B students and faculty so Sarah asked me to blog about it.

It looked like it was going to rain during the race but miraculously, the storm stopped just for the race. The weather was perfect for the race. The race was about three miles long and it looped around william street/college street and around washington terrace/usdan. After the race we all met up to take a picture and to eat pizza, bagels and cookies.

CONGRATS TO PROFESSOR HOLMES AND ARIEL FOR PLACING IN THEIR AGE GROUPS!!!

The Wesleyan MB&B team also place fifth overall :) yay for us!!!Overall the race was really fun and I hope that more people from our lab will participate next time

As everybody who works within a 50-yard radius of our lab knows, I love zygotes. THEY ARE SO CUTE. Picking zygotes is one of my favorite things to do in lab, mostly because they are SO CUTE, but also because pure diploid colonies - i.e. those that grow up from zygotes - sporulate MUCH better than mixed diploid/haploid populations - where not everybody that hits that spor plate can sporulate in the first place because HAPLOIDS DON'T DO MEIOSIS!!! I sporulated some particularly robust zygotes a few days ago and the tetrads were BANGIN'. It was delightful.

So anyway, I wanted to find a nice picture of a zygote on Google Images to post here so that you all could coo over zygotes with me, but I found Google's results unsatisfactory, so I decided to draw one myself.

Alright, so after much poking and prodding by Sarah and Tatiana…and then reading something about tears (see entry below), I have decided to make my first contribution to the blog. Bear with me.

So last week, while sitting at my job in the Science Library and doing my daily tasks (twiddling my thumbs, watching an episode of Felicity, spinning in the chair, etc.), a bored Public Safety officer strolled up to the counter and stared at me until I finally agreed to look up and make conversation. After talking about random things like the weather, Lebron James, Pattie Palace, and how he was a court martial (and not an employee at Marshalls like I originally thought he said), we somehow came upon the topic of how I was a Bio major that was working in a lab this summer. Upon hearing that, the excitement could not have been more evident on his face.

Excited Public Safety Officer: Do you guys work with mice?

Me: No, we work with yeast.

Until I said that of course.

Even so, he continued to go on and on about how he watched something on television that showed scientists growing a human ear on a mouse, and how crazy and exciting the idea was, and how amazed he was, and how he never thought such a thing was possible….and so on and so

forth. And of course, being in the field that I am, I could not help but not only feel the same excitement as the officer, but also the urge to learn more about what he was talking about (see here: http://news.bbc.co.uk/2/hi/health/1949073.stm).

But in addition to this, the conversation with the officer had me thinking. I could care less about math or history. I couldn’t initiate a conversation with anyone on a topic of interest in economics, philosophy, or religion. But everyone…yes everyone, loves at least some aspect of science.

Even if it’s just Bill Nye the Science Guy, because everyone loves him too.

Ok guys, none of my supposedly "AWESOME" "FANTASTIC" "OMG SARAH I HEAR YOU CACKLING THROUGH THE WALL LET'S BE DINO BIFFLES IN OUR BLOG FOREVS TOTES" labmates/fellow bloggers have found time in their BUSY SCHEDULES to write anything new and inspiring (Taterz, I'm glaring angrily at our shared wall, nay, FROWNING), so I'll just have to take matters into my own hands.

THAT BEING SAID. Did you know that when we create a yeast strain of interest (i.e. a precious haploid of the correct genotype and mating type obtained from approximately 1.5 billion hours of dissection), we save it for future use (i.e. for ourselves or to share with labs who might want to work with said genotype) by literally FREEZING it - sticking it in that

huge -80 degree celsius deep freezer in the alpha room (aka Esther's cave), and the yeast are totes fine when we go to get them out a month or a year or 30 years later? I THINK THAT ISSO COOL. All you have to do is get some:

-30% glycerol (about a ml per strain you want to freeze)

-Cryotubes and tough-labels (the round white ones)

-Deep freezer (-80 degrees C)

-Lab strain book

-Toothpicks

-Oh, yeast strain(s) too. Preferably useful ones.

Put a ml of glycerol in the cryotube. Glycerol is a viscous fatty acid that protects the cells from the harsh freeze-thaw cycles they endure - that's why we freeze in glycerol instead of plain water.

MY BFF GLYCEROL!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Then just place a clump of cells in the glycerol, shake it like a Polaroid picture to resuspend them, and freeze them! Then write the full genotype of the strain along with the freezer number in the strain book.

Ok that part was boring but REALLY THE COOLEST THING ABOUT ALL THIS (people who are not interested in reading protocols can start reading here) is that when you go to get them out of the freezer you don't even have to wait for the tube to thaw to remove some of the liquid!!

Karen: You can just scrape a toothpick across the top of the frozen glycerol and streak it onto your YPD plate. They'll grow right up.

Sarah: OHEMGEE, that is like SO COOL!!!!!!!! OMG, YEAST POPSICLE!!!!!!!!!! Can I try it RIGHT NOW?!?!?!?!?!??!

Wednesday, July 21, 2010

We are part of the MacQueen lab at Wesleyan University and we would like to welcome you to our lab blog, called "Cell Culture"! In case you haven't noticed, we are super nerdy and think that most everything science is fun. So don't be fooled by the title, this blog will be about the serious (and also the not so serious) aspects of cellular biology and the culture of the cell bio community. And by community we mean mostly our lab.